Is biomaRt service down?

Question

[from the mountains]

Hi everyone,

I am getting the following error message when I try to use biomaRt:

> ensembl=useMart("ensembl")
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Error in if (!grepl(x = registry, pattern = "^\n*<MartRegistry>")) { : 
  argument is of length zero

Of course I tried the website and it seems to up. I had been using biomaRt continuously until the end of last week when it started behaving this way and won't come back on.

Is the service down, and is it temporary? I am trying to get "description" and ENSEMBL IDs based on "external gene name" for a table of genes that I am working with. Would anyone recommend an alternative to biomaRt for these purposes?

*Edit

After restarting and reinstalling packages several times, I am getting some functions such as useMart and listFilters to work, which I believe retrieve information from ensembl.org, so I must be accessing the server at this point. but when I get to getBM, which is the most important function to me, I run into problems. It still says:

> xxx <- getBM(attributes=c('phenotype_description','ensembl_gene_id'), 
+              filters = 'ensembl_gene_id', 
+              values = 'ENSG00000221701',
+              mart = ensembl, verbose=T,
+              uniqueRows=F)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '0' count = '0' datasetConfigVersion = '0.6' header='1' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'phenotype_description'/><Attribute name = 'ensembl_gene_id'/><Filter name = 'ensembl_gene_id' value = 'ENSG00000221701' /></Dataset></Query>
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

Help would still be appreciated!

[ATpoint]

For me it works fine. R version 3.4.2 (2017-09-28), biomaRt_2.32.1, BioC 3.5.

R and BioC up-to-date?

[from the mountains]

hm. I'm running "R version 3.4.1 (2017-06-30)" which I updated only a few weeks ago (but well before biomaRt stopped working) and the biomaRt version is the same as yours. I tried doing all this on another server with the same R 3.4.1, biomaRt and BioC versions and actually got it working, but i'd like to use it on my workstation because I have more packages I need to use. so mystery still unsolved for me.

[Jean-Karim Heriche]

This could be a proxy settings issue. Check the biomaRt users guide for possible solutions.

Answer 1

[Mike Smith]

If that website is working for you then BioMart is up working, but something isn't working in your R session. By default biomaRt will try to redirect you to your local mirror, which if your location is correct will be either uswest.ensembl.org or useast.ensembl.org Perhaps you can try forcing it to use the central version using:

useMart(biomart = "ensembl", 
         host = "www.ensembl.org", 
         ensemblRedirect = FALSE)

[from the mountains]

Thanks for your comment. It's a good suggestion but didn't work, and I actually think my connection to the service is working, but for some reason the message shows as not connecting when I try to use certain functions.

[GenoMax]

That particular example (ENSG00000221701) is deprecated in the database (`Ensembl gene ENSG00000221701 is no longer in the database but it has been mapped to 1 deprecated identifier"). So I get this,

Parsed results:
[1] Phenotype description Gene stable ID       
<0 rows> (or 0-length row.names)

If you use a current gene ID, things work.

[from the mountains]

If that were the only issue then I would get the message that you are getting. Before this type of issue was occurring, I was getting that type of message (an empty result). I also tried other IDs and other filters and value types, and still get the same error.

[Mike Smith]

To try and understand this a bit more, what to you get back if we strip away all the biomaRt interface, and just directly submit the query to the Ensembl server? You can view code to do this here (Biostars seems to auto edit the XML if I include it here directly)

I get the following if I format the return nicely:

> message(rcurl_return)
Phenotype description   Gene stable ID
Ear-patella-short stature syndrome  ENSG00000094804
Meier-Gorlin syndrome 5 ENSG00000094804

[from the mountains]

I get an error like this:

Error in .postForm(curl, .opts, .params, style) : 
embedded nul in string: '<U+FEFF><!--Detected and blocked with Kaspersky Lab-->\r\n<html>\r\n<head>\r\n\t<meta http-equiv='content-type' content='text/html;charset=utf-8'>\r\n\t<title>Kaspersky Endpoint Security 10 for Windows</title>\r\n\t<style type="text/css">\r\nhtml,body{height:100%}\r\n\r\nbody{width:100%;min-height:100%;margin:0;padding:0;color:#2C2C2C;font:normal 11px tahoma;background:#FFF}\r\n\r\nform{margin:0}\r\ntable,input,select{font:normal 100% tahoma}\r\nimg{border:0;margin:0}\r\ntable{border-collapse:collapse}\r\na{color:#62707D}\r\n\r\n.t,tr.t td{vertical-align:top}\r\n.m{vertical-align:middle}\r\n.b,tr.b td{vertical-align:bottom}\r\ntr.t td td,tr.b td td{vertical-align:auto}\r\n.l{text-align:left}\r\n.c{text-align:center}\r\n.r{text-align:right}\r\n\r\n.nobr{white-space:nowrap}\r\n\r\n.rel{position:relative}\r\n.abs{position:absolute}\r\n.fl{float:left}\r\n.fr{float:right}\r\n.cl{clear:both}\r\n\r\n.w100{width:100%}\r\n.h100{height:100%}\r\n\r\nbig,.big{fon

which is probably indicating the fact that my own anti-virus software is blocking the signal. i think i am getting close to the root of the problem! Thank you!

[GenoMax]

Pwned by your own software!